Hepatitis C is a chronic liver disease affecting an estimated 3% of the global population, and is caused by the hepatitis C virus. Patients infected with the virus run an 85% risk of developing cirrhosis of the liver and of these, 20% will subsequently progress to hepatocellular carcinoma. HCV is recognized as a major cause of end-stage liver disease and the leading cause of liver transplantation in the developed world [Davila, J. A., et al. (2004) Gastroenterology, 127, 1372-1380; Liu, C. L. and Fan, S. T. (1997) Am. J. Surg., 173, 358-365; Garcia-Retortillo, M., et al. (2002) Hepatology, 35, 680-687; Brown, R. S. (2005) Nature, 436, 973-978]. Transplantation is not curative, since HCV-infected transplant recipients infect their donor livers. The disease burden and mortality related to HCV have risen substantially in the last decade and are predicted by the Centre for Disease Control and Prevention to increase further as the population infected, prior to widespread blood screening, ages.
The HCV genome encodes only 10 viral proteins, namely the structural proteins E1, E2 and C, and the non-structural proteins p7, NS2, NS3, NS4a, NS4b, NS5a and NS5b. The NS3 protein is a bi-functional enzyme with a serine protease domain at the N-terminus and an ATP dependent helicase domain at the C-terminus.
The nomenclature set forth in Simmonds et al., (1993) J Gen Virol, 74(Pt. 11):2391-2399 is widely used and classifies HCV isolates into six major genotypes 1 to 6 with two or more related subtypes, e.g., 1a, 1b. Additional genotypes 7-10 and 11 have been proposed but the phylogenetic basis on which this classification is based has been questioned, and thus type 7, 8, 9 and 11 isolates have been reassigned as type 6, and type 10 isolates as type 3 (see Lamballerie et al, J Gen Virol, 78(Pt.1):45-51 (1997)). The major genotypes have been defined as having sequence similarities of between 55 and 72% (mean 64.5%), and subtypes within types as having 75%-86% similarity (mean 80%) when sequenced in the NS5 region (see Simmonds et al., J Gen Virol, 75(Pt. 5):1053-1061 (1994)).
Of the six known genotypes of HCV, genotypes 1a and 1b are the most prevalent worldwide, followed by 3 and 6. The order of genotypic incidence in the UK is 3a (37.2%), 1a (30.7%), 1b (18.4%) and 2b (6.1%) which account for 92.4% of the reported cases, while in the USA 94.3% of reported infections are caused by the 1a (78.9%) and 1b (15.4%) genotypes [HCV database website at http://hcv.lanl.gov/].
The standard therapy for HCV is under review following the approval of telaprevir and boceprevir. The nature and duration of the treatment is dependent on which genotype being treated. For the treatment of infection with HCV genotype 4, the treatment regime remains a combination of weekly injections of pegylated interferon α and daily oral administration of ribavirin for a period of 48 weeks. For the treatment of infection by HCV genotype 1, the treatment regime comprises the administration of pegylated interferon α and the twice daily oral administration of ribavirin plus the three times daily oral administration of telapravir or boceprevir. For the treatment of infection by HCV genotypes 2 and 3, the treatment regime comprises the administration of pegylated interferon α and twice daily oral administration of 400 mg of ribavirin for twenty four weeks. The treatment of HCV infections is costly and is associated with numerous severe side effects, including psychiatric disorders (depression, headaches), neutropaenia, pancreatitis, diabetes, hypersensitivity reactions, haemolytic anaemia and fatigue. Ribavirin has been shown to be teratogenic in all animals tested and is contraindicated during pregnancy. Moreover, according to NICE, the treatment with pegylated interferon α ribavirin is only successful in 54-56% of patients infected with the 1a and 1b genotypes, leaving a large group of patients with no treatment alternatives.
Host genetic factors have been found to influence treatment outcome. In particular, a single nucleotide polymorphism (SNP) on chromosome 19, rs1297980, has been shown to have a strong association with response to current standard of care. Patients with the CC genotype of rs1297980 had greater than two-fold likelihood to achieve SVR than patients with non CC genotype infected with genotype 1 HCV (Ge et al., Nature 2009; 461:399-401). The trend was also evident in patients infected with GT2 and 3, though the effect was attenuated (Mangia et al, Gastroenterology (2010) 139(3):821-7).
The approval in the US and the European Union of the two NS3/4a active site protease inhibitors, telaprevir and boceprevir, is providing more treatment options to patients, with the National Institute for Clinical Excellence (NICE) issuing guidelines for their use. Both compounds show dramatic and sustained decreases in viral RNA levels in patients, but suffer from poor PK profiles and require high dosing regimes twice or thrice daily. In addition, both compounds lead to the emergence of resistance mutations [Sarrazin, C., et al. (2007) Gastroenterology, 132, 1767-1777; Kim, A. Y. and Timm, J. (2008) Expert Rev Anti Infect Ther., 6, 463-478]. As both compounds bind in the same region of the protease enzyme, mutants demonstrate cross resistance. Alternative therapies based on other HCV molecular targets, as well as second wave and second generation protease inhibitors are at earlier stages in clinical trials. Clinical experience suggests that emerging resistance is likely to be a major problem with most agents, with the possible exception of nucleot(s)ide based inhibitors of NS5b polymerase [Le Pogam, S., et al. (2010) J. Infect Dis. 202, 1510-9]. First-line therapies are likely to be combinations of effective agents that demonstrate differential cross resistance [Sarrazin, C. and Zeuzem, S (2010) Gastroenterology, 138, 447-462].
Inhibition of the NS3/4a protease activity by small active site directed molecules has been shown to halt viral replication in vitro, in the replicon cell-based assay, in the chimeric mouse model and most importantly in the clinic [Lin, C., et al. (2006) Infect Disord Drug Targets. 6, 3-16; Venkatraman, S., et al. (2006) J. Med. Chem. 49, 6074-6086; Zhou, Y., et al. (2007) J. Biol. Chem. 282, 22619-22628; Prongay, A. J., et al. (2007) J. Med. Chem. 50, 2310-2318; and Hezode, C., et al. (2009) N. Engl. J. Med. 360, 1839-49.
The HCV NS3 NTPase/helicase functions have also been extensively studied and are considered as potential targets for antiviral therapy [Frick, D. N. (2007) Curr. Issues Mol. Biol., 9, 1-20; Serebrov, V., et al. (2009) J. Biol. Chem., 284 (4), 2512-21. However, no agents are reported to be in clinical development (Swan T. and Kaplan, K. (2012) Hepatitis C Drug Development Goes from Pony Ride to Rocket Launch—The pipeline report 2012 at http://www.pipelinereport.org/toc/HCV).
Agents that inhibit helicase function by competing with the nucleic acid substrate have also been reported [Maga, G., et al. (2005) Biochem., 44, 9637-44]. A recent publication by the group of A. M. Pyle, suggests that the full length NS3 protein must undergo a conformational change to facilitate the formation of the functional complex between the enzyme and substrate RNA [Ding, S. C., et al. (2011) J. Virol., 85(9) 4343-4353]. They propose that an extended conformation, also necessary to allow access of substrates to the protease active site, represents the functionally active form of the full length protein for RNA unwinding. Further support for the extended conformation and protease domain interaction with RNA comes from a study that reports the specific interaction of viral RNA with the NS3 protease active site [Vaughan, R. et al. (2012) Virus Research, 169(1), 80-90, RNA binding by the NS3 protease of the hepatitis C virus, available on line at http://dx.doi.org/10.1016/j.virusres.2012.07.007].
Jhoti et al. Nature Chemical Biology, volume 8, number 11, pp 920-925, 2012, doi:10.1038/nchembio.1081, available online (the entire contents of which are incorporated herein by reference) reports the discovery of a highly conserved novel binding site located at the interface between the protease and helicase domains of the Hepatitis C Virus (HCV) NS3 protein. This site is reported to have a regulatory function on the protease activity via an allosteric mechanism. Jhoti et al. propose that compounds binding at this allosteric site inhibit the function of the NS3 protein by stabilising an inactive conformation and thus represent a new class of direct acting antiviral agents.